The Align Contigs tool provides a platform to easily visualize and edit contigs. It is one of the most important tools in the finishing package and also the tool with most functionalities. An alignment of contigs is performed using BLAST against either a reference sequence, or if no reference sequence is available, the contigs themselves.
When aligned to a closely related reference sequence, it becomes visible how the contigs are located relative to each other, which makes misassemblies, repeats and overlaps between contigs clear. When contigs are aligned to themselves, the main application of the contig alignment is identification of potential overlapping contigs that can be merged.
The result of the alignment can be viewed as both a list of matches and as a read mapping where contigs are represented as reads. Through different views in the Align Contigs tool it is possible to join, split and edit contig sequences, view the read mapping of a contig, remap all mapped reads to one or more contigs, and replace all mapped reads with reads from one or more datasets.